Indian Journal of Biochemistry 

& Biophysics

 

Total visitors: 2,944  since 05-06-06

 

 

CONTENTS

 

 

Papers
1/f Correlations in viral genomes – A Fast-Fourier Transformation (FFT) study	137
T Shashi Rekha and Chanchal K Mitra*
Regulation of MAL1+ gene expression encoding maltase in Schizosaccharomyces pombe by added inositol	143
Shumin Yao, Zhenming Chi* and Susu He
Effect of denaturants on the structure and activity of 3-hydroxybenzoate-6-hydroxylase	148
S Sumathi* and Dipak Dasgupta
Quantitative structure-activity relationship (QSAR) analysis of a series of indole analogues as inhibitor for human group V secretory phospholipase A2	154
G OmPraba and D Velmurugan*
Metabolic and physiologic characteristics of skeletal muscle determine its response to clenbuterol treatment	160
Santosh Sundal, Surender S Katoch and Sushma Sharma*
Augmented bone-matrix formation and osteogenesis under magnetic field stimulation in vivo XRD, TEM and SEM investigations	167
Praveen Singh*, Rakesh C YashRoy and M Hoque
Vibrational dynamics of morphine in relation to Leu5- and Met5-enkephalins	173
Neeraj Misra*, Onkar Prasad and Leena Sinha
Notes
Bemisia tabaci feeding induces pathogenesis-related proteins in cassava (Manihot esculenta Crantz)	182
Binu Antony* and M S Palaniswami
Biophysical studies on the liposome-albumin system	186
Mohammed S Al-Ayed
Trendys Meeting Report 2005	190
Instructions to Authors	194

 

——————

*Author for correspondence

 

 

 

 

 

 

AUTHOR INDEX

 

 

 

 

                                                   Papers

 

 

 

 

 

Indian Journal of Biochemistry & Biophysics

Vol. 43, June 2006, pp. 137-142

 

1/f Correlations in viral genomes – A Fast-Fourier Transformation (FFT) study

T Shashi Rekha and Chanchal K Mitra*

Department of Biochemistry, University of Hyderabad, Hyderabad 500 046, India

Received 29 September 2005; revised 05 April 2006

We have studied the presence of long-range correlations in the complete genomes of ten different dsDNA viruses and Saccharomyces cerevisiae (bakers’ yeast) chromosome I. We have also studied the correlation between the distribution of the gene length and the domain of “1/f region” of their genomes. Linear regression analysis was done for the power-law region of these organisms and the slope values obtained were ~ -1, which signify the existence of “1/f noise” in the low and medium (intermediate) frequency regions. This suggests the presence of long-range correlations in their genomes. The presence of 1/f noise in a given frequency interval indicates the existence of a fractal (self-similar) structure in the corresponding range of wavelengths. The results of our study suggest that genes have correlations within themselves, and the correlations appear to be related with the scaling exponent a.

Keywords: 1/f noise, DNA sequence, Power spectrum, Long-range correlations.

*E-mail: c_mitra@yahoo.com

 

 

Indian Journal of Biochemistry & Biophysics

Vol. 43, June 2006, pp. 143-147

 

 

Regulation of MAL1⁺ gene expression encoding maltase in
Schizosaccharomyces pombe by added inositol

Shumin Yao, Zhenming Chi* and Susu He

UNESCO Chinese Center of Marine Biotechnology, Ocean University of China, Yushan Road No.5, Qingdao, 266003, China

Received 14 October 2005; revised 14 March 2006

In this study, the effects of inositol addition on maltase activity and expression of MAL1⁺ gene encoding maltase in Schizosaccharomyces pombe were investigated. The maximum specific maltase activity was observed, when the concentration of inositol reached 6.0 mg/ml in the synthetic medium containing 2.0% glucose. At 1.0 mg/ml inositol concentration, the maltase activity continuously decreased, as initial glucose concentration was higher than 0.1%. mRNA encoding maltase and phosphatidylinositol (PI) content were higher in the cells grown in the synthetic medium with 6.0 mg/ml of inositol and 2.0% glucose than those with 1.0 mg/ml of inositol. These results demonstrated that higher inositol concentration in the synthetic medium could derepress MAL1⁺ gene expression in S. pombe and PI might be involved in derepression of MAL1⁺ gene expression in S. pombe probably by PI-type signalling pathway.

Keywords: Schizosaccharomyces pombe, Phosphatidylinositol, Derepression, MAL1⁺ gene encoding maltase, Inositol

*E-mail: zhenming@sdu.edu.cn

 

 

Indian Journal of Biochemistry & Biophysics

Vol. 43, June 2006, pp. 148-153

 

Effect of denaturants on the structure and activity of
3-hydroxybenzoate-6-hydroxylase

S Sumathi* and Dipak Dasgupta

Department of Biochemistry, Indian Institute of Science, Bangalore 560 012

Received 20 September 2005; revised 17 April 2006

The effect of denaturants such as urea, sodium dodecylsulphate (SDS), guanidinium hydrochloride (Gu.HCl) on the structure of enzyme 3-hydroxybenzoate-6-hydroxylase was studied using intrinsic fluorescence and far and near-UV-CD spectroscopic techniques. Also, activity profiles of the enzyme, as a function of increasing concentrations of denaturants were studied. The far-UV CD spectrum of the enzyme did not show appreciable alterations in the presence of urea, SDS or Gu.HCl, thereby suggesting that the protein does not undergo gross conformational changes in its a-helical secondary structure. The treatment of enzyme with 2 M urea resulted in almost complete loss of catalytic activity, accompanied by the reduction of emission fluorescence of enzyme. Similarly, treatment with 0.01% SDS also caused almost complete loss of activity and quenching of enzyme fluorescence as well as a red shift in the emission peak. In addition, reduction in the intensity of near-UV-CD spectrum, especially at 280 nm was observed. About 70% of the activity was lost by treatment with 20 mM Gu.HCl, accompanied by quenching of intrinsic fluorescence of the enzyme. The change in intrinsic fluorescence of the enzyme in the presence of 5 mM-100 mM Gu.HCl could be correlated to progressive loss of catalytic activity. Thus, intrinsic fluorescence (due to tryptophan residues) could be used as an effective probe to provide an insight into the relation between the activity and subtle conformational changes of the enzyme. The results suggested that denaturants caused very slight conformational changes in the enzyme that perturbed the microenvironment of aromatic amino acid residues such as tryptophan accompanied by reduction or loss of catalytic activity.

Keywords: 3-Hydroxybenzoate-6-hydroxylase, Circular dichroism, Fluorescence, Denaturants, Guanidinium hydrochloride, Sodium dodecyl sulphate, Urea

 

*E-mail: sumathis@iitb.ac.in

 

 

 

Indian Journal of Biochemistry & Biophysics

Vol. 43, June 2006, pp. 154-159

 

 

Quantitative structure-activity relationship (QSAR) analysis of a series of indole analogues as inhibitor for human group V secretory phospholipase A₂

G OmPraba and D Velmurugan*

Department of Crystallography and Biophysics, University of Madras, Guindy Campus, Chennai 600 025, Tamilnadu, India

Received 29 November 2005; revised 21 April 2006

Phospholipase A₂s (PLA₂) are a class of enzymes, which catalyze the hydrolysis of membrane phospholipids at the sn-2 position to release fatty acids and lysophospholipids. When the fatty acid is arachidonic acid (AA), a complementary metabolism leads to pro-inflammatory mediators collectively known as eicosanoids. Thus, inhibiting PLA₂ activity remains a prime target for the development of new drugs for the treatment of inflammation-related diseases. More than one type of PLA₂s plays a major role in inflammatory disease conditions. In the present study, quantitative structure-activity relationship (QSAR) study was performed for a series of 48 Me-indoxam derivatives as human group V PLA₂ (hVPLA₂) inhibitors, using molecular operating environment (MOE) software. The hVPLA₂ is a secretory PLA₂ (sPLA₂), involved in eicosanoid formation in inflammatory cells such as macrophages and mast cells. These studies have come out with three good predictive models (r = 0.82-0.84), which are cross-validated (r_cv = 0.68-0.70) by leave-out-one method (Loo). The positive correlation of spatial descriptor Pmi_z with inhibitory activity shows that proper orientation of the substitution at R position towards Z-axis is necessary to facilitate the possible interactions of the indole core with active site residues of the PLA₂ enzyme. The negative contribution of b_rotN (atom and bond count-type descriptor) suggests that increasing flexibility conferred by the R substitution is detrimental for the activity. In addition to the hVPLA₂ inhibitory activity is found to be highly influenced by molecular size, energy and polarity of the Me-indoxam derivatives.

Keywords: Phospholipase A₂, QSAR, hVPLA₂ inhibitor, Indole analogs, Me-indoxam.

 

*E-mail: d_velu@yahoo.com

 

 

 

Indian Journal of Biochemistry & Biophysics

Vol. 43, June 2006, pp. 160-166

 

Metabolic and physiologic characteristics of skeletal muscle determine its response to clenbuterol treatment

Santosh Sundal, Surender S Katoch and Sushma Sharma*

Department of Biosciences, Himachal Pradesh University Summer Hill, Shimla 171 005, India

Received 15 May 2005; revised 03 May 2006

β-Adrenoceptor agonists are reported to induce skeletal muscle hypertrophy and hence serve as valuable adjunct to the treatment of wasting disorders. In the present study, we attempted to find out whether metabolic and physiologic characteristics of fibres are important in determining skeletal muscle response to clenbuterol (an adrenergic receptor agonist) therapy, as proposed in the treatment of wasting disorders. The treatment of mice with clenbuterol (2 mg/kg body wt for 30 days) resulted in skeletal muscle hypertrophy, more common amongst fast-twitch glycolytic fibres/muscle, with increase in body mass and a parallel rise in muscle mass to body mass ratio. Measurement of fibre diameters in soleus (rich in slow-twitch oxidative fibres), ALD or anterior latissimus dorsi (with a predominance of fast-twitch glycolytic fibres) and gastrocnemius (a mixed-type of muscle) from clenbuterol-treated mice for 30 days revealed noticeable increase in the per cent population of narrow slow-twitch fibre and a corresponding decline in white-type or fast-twitch glycolytic fibres in gastrocnemius and ALD. As revealed by counting of muscle cells in soleus, narrow red fibres declined with corresponding increase in white-type glycolytic fibres population. A significant decline in the succinic dehydrogenase activity was observed, thereby suggesting abnormality in oxidative activity of skeletal muscles in response to clenbuterol therapy.

Keywords: Clenbuterol, Metabolic and Physiologic characteristics, Skeletal muscles

*E-mail: sushma_bio_sci@rediffmail.com

 

Indian Journal of Biochemistry & Biophysics

Vol. 43, June 2006, pp. 167-172

 

 

Augmented bone-matrix formation and osteogenesis under magnetic field stimulation in vivo XRD, TEM and SEM investigations

Praveen Singh^1*Π, Rakesh C YashRoy¹ and M Hoque²

¹Biophysics and Electron Microscopy Section, ²Surgery Division, Indian Veterinary Research Institute,
Izatnagar-243122, UP, India

Received 02 June 2005; revised 25 January 2006

Bone is a composite biomaterial, which is formed, when proteins constituting collagen fibers attract calcium, phosphate and hydroxide ions in solution to nucleate atop the fibers. It grows into a hard structure of tiny crystallites of hydroxyapatite, aligned along the long axis of collagen fibers. The present work reports the stimulating effect of static magnetic field on microstructure and mineralization process of bone repair. A unilateral transverse fracture of mid-shaft of metacarpal was surgically created in healthy goats under thiopental sedation and xylocaine analgesia. Two bar magnets (~ 800 gauss/cm² field strength) were placed across the fracture line at opposite pole alignment immobilized in Plaster of Paris (POP) splint bandage for static magnetic field stimulation. Radiographs were taken at weekly intervals up to 45 days. Results show that formation of extra-cellular matrix and its microstructure can be influenced by non-invasive physical stimulus (magnetic field) for achieving an enhanced osteogenesis, leading to quicker regeneration of bone tissue in goats. X-ray diffraction (XRD) patterns of treated (magnetic field-exposed) and control samples revealed the presence and orientation of crystalline structures. Intensity of diffraction peaks corresponding to 310 and 222 planes were enhanced with respect to 211 families of reflections, indicating preferential alignment of the crystals. Also, the percent crystallinity and crystal size were increased in treated samples. The study provides a biophysical basis for augmented fracture healing under the influence of semi-aligned static magnetic field applied across the fracture line.

Keywords: Fracture healing, Static magnetic field, Hydroxyapatite, Collagen fibers, XRD pattern, Electron microscopy

          *E-mail singh@belab.ed.kyushu-u.ac.jp

 

 

Indian Journal of Biochemistry & Biophysics

Vol. 43, June 2006, pp. 173-181

 

Vibrational dynamics of morphine in relation to Leu⁵- and Met⁵-enkephalins

 

Neeraj Misra^{* 1}, Onkar Prasad¹ and Leena Sinha²

¹Department of Physics, Lucknow University, Lucknow, 226 001, India

²Mahila P G College, Aminabad, Lucknow, India

Received 06 October 2005; revised 20 April 2006

A complete normal coordinate analysis of morphine using Wilson’s GF matrix method and Urey Bradley force field has been carried out to understand the dynamical behaviour of morphine in relation to Leu⁵- and Met⁵-enkephalins. In addition, charge distribution on different atoms of morphine, along with that of Leu⁵- and Met⁵-enkephalins using CNDO/2 method is also reported. The similarity in charge distribution on some of the sites of these molecules is indicative of the possible interactions at the same receptor site. It is surmised that the recognition and interaction of active sites with the receptor must be dynamical in nature and for this the modes involving the active sites should play an important role. It is found that the binding to receptors is not static, but a dynamic process.

Keywords: Morphine, Opioid peptides, Vibrational dynamics, Charge distribution, Receptor interaction

 

         *E mail: neeraj@vedicfire.com; misraneeraj@gmail.com

 

Notes

 

 

 

 

Indian Journal of Biochemistry & Biophysics

Vol. 43, June 2006, pp. 182-185

 

Bemisia tabaci feeding induces pathogenesis-related proteins in cassava
(Manihot esculenta Crantz)

Binu Antony*and M S Palaniswami

Division of Crop Protection, Central Tuber Crops
Research Institute

Thiruvananthapuram 695 017, Kerala, India

Received 18 August 2005; revised 19 January 2006

Cassava (Manihot esculenta Cranzts) plants fed upon by whitefly Bemisia tabaci showed increased levels of pathogenesis-related (PR) proteins, such as β-1, 3-glucanase, peroxidase and chitinase activities, as compared to uninfested plants. The enzymes increased in specific activities from 2 to 7 fold and protein content in leaf extracts decreased in whitefly-infested plants, compared to uninfested plants. Among the three PR proteins, B. tabaci feeding induced significantly higher β-1, 3-glucanase activities, when compared with other two PR proteins. Study also discussed the possible application of PR proteins in whitefly control program.

Keywords: Bemisia tabaci, Pathogenesis-related proteins, Cassava

*E-mail: binuantony1@yahoo.co.in

 

 

Indian Journal of Biochemistry & Biophysics

Vol. 43, June 2006, pp. 186-189

 

Biophysical studies on the liposome-albumin system

Mohammed S Al-Ayed

Physics and Astronomy Department, College of Science,
King Saud University, P.O. Box 2455,
11451 Riyadh, Kingdom of Saudi Arabia

Received 24 October 2005; revised 03 May 2006

The potential use of liposomes as a delivery system is still limited by the poor understanding of their interaction mechanisms with biological media. In the present work, interaction between bovine albumin (BA) and liposomes was studied using phase transition and dielectric measurements as well as solubilization process using non-ionic detergent octylglucoside (OG). After liposomes were incubated with diluted and concentrated BA, phase transition, characterizing the liposome membrane exhibited a shift towards higher temperatures, together with initiation of multiple phase transitions. The relaxation time of liposome membrane molecules also increased in a concentration-dependent manner. The solubilization profiles of incubated samples also showed remarkable changes, especially in beginning of solubilization stages. Moreover, amount of detergent needed to completely solubilize membrane was also increased. It was concluded that BA significantly altered the physical state of liposome membrane, which may be attributed to BA interaction with liposomes surface and/or by its incorporation within the bilayer membrane.

Keywords: Liposomes, Dielectrics, Phase transition, Solubilization

E-mail: malayed@ksu.edu.sa

Indian Journal of Biochemistry & Biophysics

Vol. 43, June 2006, pp. 190-193

 

TRendys Meeting Report 2005

 

The Human Genome Project has created an immortal landmark in the never-ending pathway of biology, as it presents us with the sequence of the entire human genome. This was like a much awaited opening up of a hitherto closed door and now, science has stepped into new facets of research fields, be it in molecular genetics, disease diagnostics, drug designing or proteomics. This was precisely the notion of discussion with which met the eminent scientists and professors from all over the country for the Twelfth Annual Meeting of “TRendys in Biochemistry” held on 29^th and 30^th Dec, 2005 at Indian Institute of Chemical Biology (IICB), Kolkata. TRendys has always been an eye opener, especially for the students and indeed, they gathered in hundreds at the IICB Lecture Theatre, as Dr. H K Majumder (IICB, Kolkata), the convenor of the meeting, delivered his welcome address. Prof. K Subba Rao (University of Hyderabad) briefed up the concept of TRendys.

 

Dr. Prakash (CFTRI, Mysore) in his TRendys Oration lecture “Proteins – Stabilization Energy and Thermodynamics – How are they related to Society!?” highlighted the effect of solvent and macro-molecular stabilization and its energy with thermodynamic point of view. A number of methods stabilize macromolecules, mainly by altering the external conditions of the molecule or by genetically manipulating the amino acids. He emphasized on altering the external conditions in such a way as to induce stabilization of the macromolecule, especially multi-subunit proteins and enzymes. The structure of water (the bulk solvent) and its interaction with the amino acid residues have a major role in the stabilization of the proteins. These interactions are generally inter-linked with enthalpy-entropy compensation and the thermodynamic state of the protein. Any additive, which alters the molecular structure of water and, in turn, perturbs the water-amino acids interaction has normally a profound effect on the thermal and even activity stabilization of proteins/enzymes. Certain reagents such as polyhydric alcohols and some of the sugars have a significant effect on the potential hydration and also on the preferential interaction of these small molecules and their indirect effect on water structure. Solvents may affect proteins through viscosity and osmotic pressure. The latter determines the hydration state of the protein. It appears that surface hydration layer and a few internal water molecules are vital to the normal protein function, conferring to it internal stability and flexibility. He mentioned that a consortium of enzymes and proteins for specific use in target foods could be built by keeping the effects of co-solvents in perspective in stabilization of the proteins, which would result in better functional properties of foods. Lastly, he emphasized the role of food technology, nutrition and healthy foods and relation between them. He also explained the Indian traditional food scenario and fortification of foods from societal angle in India and also CFTRI role for outreach to Tsunami victims.

A short address from Prof. T Ramasarma (IISc, Bangalore), who conceived the TRendys type of presentations, paved the way for the eagerly awaited scientific session. He said that the youngsters should try to take up novel ideas for their research, instead of simply continuing their pre or post-doctoral research lines and this requires good and imaginative thinking which will pave way for quality improvement in the Indian science. For the next two days, IICB lecture theatre happened to be an abode of novel thoughts, newer perceptions and research strategies leading to the fruits of scientific endeavor.

The scientific session was multifaceted, enriched by lectures on genomics, fundamental functional works, as well as the indispensability of computational study in biology. One of these facets was to help the students, who were from different fields of basic science to conceptualize “genomics”, more so, since the meet was supposed to be based on the idea of research in the post-human genome sequencing era. Indeed, there were three fine lectures fundamentally on the concept of genomics.

Dr. Nitai P Bhattacharyya (Saha Institute of Nuclear Physics, Kolkata) through his talk on “Applications of Human Genome Sequence Information in Biomedical Researches” put up in a nice storyline, the history of human genome sequencing project, the aims and strategies undertaken, the information, in general as provided by the sequence ‘read’ as well as the possibilities of research after genome sequencing, exemplifying the likes of HAPMAP and medical re-sequencing (MRS) projects. He explained how mutations differ from polymorphisms on the basis of frequency of occurrence. He also talked about single nucleotide polymorphisms (SNPs), the most abundant variations in the human genome and possible effects of various SNPs on gene function, depending on their location. He presented some of his own research data to show how his group is using expansion of CAG/CTG repeats as a tool for identification of various neurodegenerative diseases as well as predicting the prevalence of these diseases in India.

In fact, Dr. Susanta Roychaudhury (IICB, Kolkata) dealt with these SNPs as he presented his talk on “Mapping Susceptibility Alleles in Complex Diseases”. In complex diseases, basic Mendelian pattern of inheritance does not hold good and multifactorial determination of a disease is a must. He lucidly explained how in case of such diseases, some characteristic signature motifs can be identified to recognize the susceptibility locus, specifically true in case of the low penetrance genes. Herein, SNPs
could serve as important candidate as the susceptibility marker for such study, as it became apparent from his talk. He gave us an idea about how specific haplotypes, based on some selected SNPs could be informative of the susceptibility status of a particular individual for a specific disease. Some data of his own work helped his cause, when he explained how through case-control study, specific genotypes of the IL1B gene were determined to be
the risk factors for Helicobacter pylori-mediated gastric ulcer.

Dr. Partha P Majumder (Indian Statistical Institute, Kolkata) delivered his talk on “Gilbert Syndrome in India”. The syndrome represents a hepatic disease related with the reduced activity of UDP-glucuronyltransferase, as a result of which the amount of unconjugated bilirubin increases in the body, clinically manifesting a milder form of jaundice. He described how his group observed higher level of association of A(TA)₇TAA allele with the ‘Gilbert Syndrome’ patients in India than the more commonly found A(TA)₆TAA allele. Interestingly, presence of a CAT insertion upstream of the TATA box in the UGT1A1 gene promoter (encoding a specific isoform of UDP-glucoronyltransferase), in the background of the A(TA)₇TAA allele reduced the transcription efficiency of the gene considerably. This insertion, according to him alters the DNA folding in a way that diminishes transcription of the gene.

Talks regarding genomic research were also presented in a much broader perspective, to help envision a general field of research in its totality. Dr. Kunal Ray (IICB, Kolkata) through his talk on “Vision Research: The Road Ahead” presented an overall status of vision research in the post-human genome project era. He laid importance on vision research, since eye-associated problems are quite common among the genetic diseases; more so in India since 1/4th of the world’s blind population live here. He talked about the etiology, genetics and possible cure of different genetically determined eye diseases like cataract, glaucoma, retinitis pigmentosa (RP) etc. He emphasized that identification of gene defects would help to contain these hereditary diseases from spreading, but functional studies are necessary for understanding the pathology of the disease and development of suitable drugs. He also demonstrated that attention given to and progress made on understanding eye diseases is based on the nature of underlying problem taking examples from color vision, cataract, RP, glaucoma etc. He also stressed that solution to a biological problem is not necessarily restricted to tackling this issue only biologically – for example, multitude of potential gene therapy protocols for RP vs attempts to replace damaged retina with a prosthetic device.

Prof. K Subba Rao (University of Hyderabad) dealt with a very interesting topic viz. “p53 and Cancer: Friends or Foes?” and talked about the versatility of the p53 gene with respect to cellular functions and its downstream genes, it regulates. He opined that in the organisms with renewable tissues, p53 activity might be optimally balanced to prevent the development of cancer as well as the premature occurrence of the ageing phenotype. He attempted to relate recent observations from different laboratories that overexpression of p53 may reduce the tumor incidence, but may accelerate the aging phenotypes. p53 being the guardian of genome controls a number of genes which play important regulatory roles in the cellular system.

However, till date there are numerous genes, which have not been annotated functionally. Dr. Arun Lahiri Majumder (Bose Institute, Kolkata) took up this very issue in his talk “Functional Assignment of Gene(s) in the Post-Genomic Era: Synechocystis Inositol Metabolizing Gene(s) as Example”. A daunting task to the biologists in the post-genomic era is assignment of function to the sequenced genome. Assignment of gene function in an identified ORF is usually done by sequence comparison of the candidate ORF with the already known genes with defined function available in the database. However, he pointed out that a large percentage of sequenced genome possesses ORFs, whose function cannot be assigned based on such sequence comparison. Such ORFs are often designated as ORFans. He elaborated how he used a combination of bioinformatic, molecular genetic and mass spectrometry data and eventually now, the, unassigned hypothetical ORF sll1722 from Synechocystis PCC6803 can be assigned to be L-myo-inositol-1-phosphate synthase.

The term genomics does not encompass only the coding nucleic acid sequences, but a complete idea needs an elaborate study of the regulatory region of the concerned genes as well as the proteins interacting with the regulatory regions. Thus, in today’s world, genomics, transcriptomics and proteomics walk hand in-hand. Dr. Siddhartha Roy (IICB, Kolkata), through his wonderful lecture on “Specificity of Protein-DNA Interactions” emphasized the pattern of interaction of proteins and nucleic acids; the interface as well as the formation of the DNA-protein complex (assembly) giving an example of RNA Pol II complex formation in the promoter region of the DNA. He explained in terms of energy, feasibility of a particular protein to interact with a signature motif of DNA and induce a particular pattern of DNA bending. He also dealt with the target searching for a particular protein amidst the genome and opined that the mobility of the protein seeking its target must be a random process to sustain thermodynamic feasibility.

Dr. Roy’s lecture was aptly followed by a presentation on “Protein Folding by Ribosome” by Prof. Chanchal K Dasgupta (Calcutta University, Kolkata). Ribosome folds all the proteins synthesized on it, and peptidyl transferase centre is presumably the active site for folding. He mentioned that although secondary structures are formed in polypeptide chains during synthesis, the final tertiary structure cannot be formed before dissociation of the last peptidyl tRNA to ensure full accessibility of the peptidyl transferase centre for the nascent protein. He concluded that though protein folding is accompanied by dissociation of the ribosome into its subunits, but whether this dissociation is the only mode of ribosome recycling remains to be investigated.

“New insights into the Functional Role of the Estrogen Receptor Activation Factor (E-RAF)” was the topic of discussion of Prof. R V Thampan (Rajiv Gandhi Centre for Biotechnology, Kerala). He mentioned that E-RAF is a DNA-binding protein that exists in two molecular forms E-RAF-I and -II, both of which dimerize with an estrogen receptor that does not bind to the DNA itself, but to the nuclear protein. E-RAF gene expression is regulated by both estradiol and progesterone and it reaches a peak during estrus and also during mid pregnancy. Eventually, it was found that a calcium-activated neutral protease cleaves E-RAF into two fragments ά and β – with an average molecular mass of 31 kDa. While ά fragment has the DNA binding function, β binds progesterone and cholesterol. Intracellular localization and nuclear transport of E-RAF were also the points of discussion. A docking protein 55 (dp55) is known to be involved in the nuclear entry of progesterone-E-RAF complex. He also spoke on the possibility of two functional forms of E-RAF influencing two entirely different sets of genes.

Prof. Samir Bhattacharya (Visva Bharati University, Santiniketan) in his presentation "Molecular Mechanism of Insulin Resistance” explained the basis of insulin resistance, which can lead to type 2 diabetes. In this context, he described a protein (A-Zip/F1) that blocks several classes of transcription factors in adipocyte and when expressed in the transgenic mice render them severely insulin resistant, due to non-functional adipocytes. He elucidated the role of free fatty acids (FFA), especially palmitic acid as causative agents of insulin resistance. He also described the insulin-induced cell signaling pathway in the target cells and the mechanism of FFA-induced inhibition of insulin receptor gene promoter activity. The down-regulation of the insulin receptor leads to insulin resistance and type 2 diabetes.

In the post-genomics era, with all the first hand knowledge of human genome sequence as well as many unknown channels regarding chromatin structure being revealed gradually, one of the primary aims of the scientists has been efficient drug designing that can specifically interact with a specific portion of the nucleoprotein complex in the cell.
Prof. D. Dasgupta (SINP, Kolkata) discussed this issue and in his talk, he dealt with “Chromatin Structure as Target of Drugs.” He explained in brief, the packaging of a chromatin complex from the individual histones to the higher order nucleosome structure. He suggested that the molecular basis of chromatin remodeling is dependent on different functional states of the chromatin structure. These functional states are dictated by various modifications (e.g. acetylation, methylation, phosphorylation and ubiquitination) of unstructured amino terminal tails of the core histone proteins consisting of 25-40 residues. This remodeling alters histone-DNA interaction, thereby increasing the overall accessibility of the DNA to the transcription factors. The main target of the talk was on the concept of drug-induced disruption of proper DNA-histone interaction in case of cancer cells. He gave a plethora of examples of different types of anticancer drugs like neotropsin as a groove binder drug and cisplatin as a DNA cross-linker etc. He did also discuss the effects of DNA targeting drugs upon chromatin structure as well as the biophysical and biochemical methods to examine the effects of DNA-targeting anticancer drugs upon chromatin structure.

Bioinformatics indeed has become an important part of today’s biology. Dr. Chitra Dutta (IICB, Kolkata) presented a complete in silico work, viz. “Selection-Mutation Balance in Genome Evolution”. She dealt with variations in genome composition in unicellular organisms, both inter as well as intra-genomic. To elaborate the phenomenon of codon bias, she mentioned that it represented a measure of how small a subset of codons would be used by a gene. The value may range from 61 for a gene using all codons with equal frequency to only 20 for a gene that would effectively use single codon to translate to its corresponding amino acid. Higher the selection pressure, higher is the codon bias. She held the view that factors such as directional mutation pressure, gene expressivity, and bioenergetic requirements might influence the codon bias.

An entirely new facet in TRendys 2005 was opened up by Prof. D J Chattopadhyay (University of Calcutta, Kolkata), who delivered his talk on “Synthetic Biology: Dictating Life the Way You Want”. According to him ‘Engineering of new biological components and organisms and redesigning of the existing ones with the goal of improving quality of our life’ is what we mean by synthetic biology. He expressed the need for this idealistic system, since the naturally occurring entities may not be able to address or solve all our problems related to desired biological outputs. Optimization of nature for the best benefit of humankind and its environment is the ultimate goal of synthetic biology. He showed how genome engineering could help create a self-sustaining cell model (minimal cell) having only 127 genes just sufficient to maintain protein and membrane structure. However, there are a set of predefined factors and models to ensure the success. He not only talked about the numerous challenges, but also showed the way how the scientific world plans to tackle them. It was fascinating to know that synthetic biology would need, apart from biologists and biochemists, hard core engineers and re-writers whom he pointed out to be those personnel who would test the idea that ‘natural biological systems are as such complicated and it would be better off to rebuild them from ground-up to provide engineered surrogates that are easier to understand and interact with’. This only reflects wholesomely, Dr. Kunal Ray’s views when he emphasized in the concluding note of his presentation, “Biological problems should be addressed based on a broader perspective built on multi-disciplinary approaches”.

The meeting, being attended by a good number of students, research scholars, eminent scientists and professors from varied fields, was no doubt, a great success. The fundamental ideology with which the TRendys was founded, i.e. to share general thoughts as well as novel findings, was fulfilled up to the brim and it is bound to instigate among the new blood, a passion of positive thinking, a quality to master in the field of research.

 

Kunal Ray & Mainak Sengupta

Indian Institute of Chemical Biology

Jadavapur, Kolkata 700 032

E-mail: kray@iicb.res.in / thisiskr@rediffmail.com